Related Issues (20)
- ENH: Change how the CARD database is loaded with function `load_card`
- ENH: Add progress bars to downloads with `fetch-card-db` action
- BUG: ValueError when running `collate-reads-allele-annotations`
- BUG: `sample_dict` function of `CARDAnnotationDirectoryFormat` does not include all MAGs per sample
- CI: The name of the qiime2 distro has changed and has to be updated
- TEST: Coverage is low in `_formats.py` and `utils.py`
- ENH: Adding new action to download NCBI database for AMRFinderPlus
- BUG: No module named tqdm
- ENH: New type for amrfinderplus database
- CI: Adding new CI
- ENH: New type for AMRFinderPlus annotations
- ENH: Action to annotate SampleData[MAGs] with amrfinderplus
- ENH: New action that annotates `FeatureData[Sequence]` and `FeatureData[ProteinSequence]`.
- BUG: database_format_version.txt is needed for AMRFinderplusDatabaseDirFmt
- ENH: Add GenomeData[Proteins] and GenomeData[Loci] inputs to annotate-sample-data-amrfinderplus action HOT 1
- ENH: Change `FeatureData[AMRFinderPlusAnnotation]` type
- ENH: Adding three new parameters to run_amrfinderplus_n
- CI: Codecov report does not show up on PRs
- ENH: New transformer to transform AMRFinderPlusAnnotationsDirFmt to immutable.Metadata
- REF: Create utils module.
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